Analysis of our genotypic data from a 1 M SNP GWAS identified a SNP (rs1861612) in DNER that associated with T2D at genome-wide significance (odds ratio = 1.29 per copy of the T allele, P = 6.6 x 10-8). DNER (delta/notch-like EGF repeat containing) is expressed in islets and mediates notch signaling via cell-cell interaction. Notch signaling is critical for pancreatic development. We assessed the physiologic role of DNER in a mouse -cell line in which DNER was both over-expressed and knocked down by siRNA targeting. Notch pathway specific genes, Notch1, Hes1, and Neurog3 were significantly regulated by DNER (P <0.001), suggesting that alterations in DNER mediate an effect on T2D susceptibility through the notch signaling pathway. Although DNER has not been previously reported in GWASs for T2D, NOTCH2 is a highly reproducible T2D gene in other ethnicities. Analysis of the genotypic data for associaiton with BMI identified MAP2K3 as a new gene for obesity. This gene had not been reported as being among the top signals in published GWASs from other ethnic groups, however, we requested that the GIANT study of BMI in Caucasians look at specific SNPs in their GWAS data and several SNPs did have significant associations with BMI (P = 2 x 10-4). The effect of these variants was larger in American Indians as compared to Caucasians. Combining our American Indian data with the Caucasian data provided strong associations (P = 4 x 10-9). Functional studies on MAP2K3 showed that this gene has a role in adipogenesis, which is consistent with what is currently known about MAP signaling pathways. However, we also show that constitutive expression of MAP2K3 in the hypothalamus, a key tissue for modulating food intake, is associated with an up-regulation of genes involved in inflammation. This is an intriguing finding because several recent reports have proposed a causal role of hypothalamic inflammation in high fat induced obesity, as well as cytokines eliciting effects on feeding behavior. Follow-up of additional signals from our GWAS identified variation within the FOXO1A gene that modestly associated with early-onset (onset age <25years) T2D. FOXO1A encodes the forkhead transcription factor involved in pancreatic beta-cell growth and hypothalamic energy balance; therefore, variation across the FOXO1A locus was thoroughly interogated by genotyping all tag SNPs in a population-based sample of 7710 American Indians. An intronic SNP rs2297627 associated with early-onset T2D as well as T2D onset at any age, where the T2D risk allele also associated with lower acute insulin secretion. Another intronic SNP (rs1334241, D=0.99, r2=0.49 with rs2297627) associated with maximum adulthood BMI, maximum childhood BMI and % body fat. Therefore, we propose that common variation in FOXO1A modestly affects risk for T2D and obesity in American Indians. Our GWAS in Pima Indians also identified a variant within PFKFB2 (rs17258746) that associated with BMI. PFKFB2 encodes 6-phosphofructo-2-kinase/fructose 2,6-bisphosphatase isoform 2, which plays a role in glucose metabolism. To follow-up on the GWAS, tag SNPs across PFKFB2 were genotyped in American Indians who had longitudinal data on BMI (n=6839), T2D (n=7710), diabetic nephropathy (DN; n=2452), % body fat (n=555) and insulin secretion (n=298). Two SNPs were further genotyped in urban American Indians to assess replication for DN (n=864). PFKFB2 expression was measured in 201 adipose biopsies using real-time RT-PCR and 61 kidney biopsies using the Affymetrix U133 array. Two SNPs (rs17258746 and rs11120137), which capture the same signal, were associated with maximum BMI in adulthood, maximum BMI z-score in childhood and % body fat in adulthood. The adiposity-increasing allele correlated with lower PFKFB2 adipose expression. Lower expression of PFKFB2 further correlated with higher % body fat and BMI. This allele was also associated with increased risk for DN in both cohorts of American Indians and similarly correlated with lower PFKFB2 expression in kidney glomeruli. The same allele was also associated with lower insulin secretion assessed by acute insulin response and 30-min plasma insulin concentrations. Therefore, we propose that variation in PFKFB2 appears to reduce PFKFB2 expression in adipose and kidney tissues, and thereby increase risk for adiposity and DN. To identify additional genetic variations that increase risk for DN, we performed a genome-wide association study (GWAS) in 2388 subjects (1579 full heritage and the 809 non-full heritage Pima Indians) which represented 519 DN cases (albumin-to-creatinine ratio ACR300mg/g or ESRD) and 1869 controls (ACR<300mg/g), where all cases and controls had T2D. Genotyping utilized a custom Axiom array with 494K tag SNPs which capture 92% of common coding and non-coding SNPs (minor allele frequency of 0.05) and 56% of lower frequency coding-only SNPs (0.01-0.05) identified in the Pima genome. The power to detect an association with an effect size OR=1.20 was 0.54 for a risk allele with frequency of 0.50. As anticipated by the power calculations, no single SNP achieved genome-wide statistical significance (5x10-8). Therefore, we focused on those SNPs with reproducible evidence for association in full and non-full Pima Indian samples analyzed separately, which were also predicted to have a deleterious impact on protein function. These SNPs were further genotyped in an independent sample of 902 American Indians living in urban Phoenix (157 DN cases and 745 controls). SNP rs3732666 which predicts a S361G in the FBLN2 gene showed a consistent association with DN in full heritage (OR=1.33 per copy of G allele, frequency =0.28, p=7.1x10-3) and non-full heritage Pima Indians (OR=1.55, p=5.6x10-3) from the Gila River Indian Community, and also associated with DN in American Indians from urban Phoenix (OR=1.38, p=0.048). A meta-analysis of all 3 cohorts demonstrated the strongest association with DN OR=1.39, p=2.3x10-5. FBLN2 encodes the extracellular matrix remodeling protein fibulin2, which is a modulator of transforming growth factor b1 (TGFb1) and vascular endothelial growth factor a (VEGFA) pathways. In vitro studies of this missense variant in FBLN2 in cultured kidney cells are ongoing to establish whether the S361G variant affects TGFb1 and/or VEGFA signaling. Knowledge of the genetic basis of DN may lead to a better understanding of why some individuals with T2D develop DN, while others do not.